A question of time
by LMXB
Summary: Waking to a world that is similar but different, John has to decide what he wants and where he'll fit in. A John centric story.
1. Chapter 1

**Disclaimer:** I do not own SGA or the characters.

 **A/N:** This is set after the series ended, but assumes the City got back home.

* * *

"Welcome back Colonel." A man smiled as John cracked his eyes open.

"Where am I?" The Colonel asked, not recognising the man talking to him.

"You don't recognise it?" The man questioned.

Attempting to sit up John scanned the room, which was similar to the Atlantis infirmary. The subtle differences were enough to make John tense as his mind ran wild going through the different possibilities from a bad dream to replicators.

"Your eyes don't lie. This is the Atlantis infirmary Colonel, albeit sporting a few changes from last time you saw it." The stranger said.

"Including you." John pointed out.

"Indeed. I apologise for not introducing myself. I am Dr Steven Doyle. I am the CMO."

"The CMO?" John asked sceptically. "Where's Keller?"

"Gone. As I said a lot has changed round here." The man explained. "Get some rest, everything will be explained when you are stronger."

John started to argue, only to find his eyelids getting heavy. Unable to stay conscious he fell back into darkness.

-00-

"You're awake." Doyle greeted. "I was beginning to get worried. How are you feeling?"

"Like I need answers." John replied tensely.

"Which you will get shortly." The doctor said. "But first I need to check you are fit enough."

"Fit enough?"

"Mentally and physically. I'm just going to run a couple more scans and then ask a few basic questions."

"Such as the location of Atlantis or my home world?" John asked convinced he was involved in an elaborate hoax.

"I assure you Colonel you are on Atlantis and we all know full well where Earth is. If you want I can give you the exact coordinates?"

"What I want is to understand what is going on and where Keller, McKay, Teyla and Ronon are." John said irritably.

"As soon as I have run these tests I'll take you to the briefing room where you'll get all the answers you need." Doyle replied. "So shall we start?"

"Fine."

"Full name and rank?" Doyle asked.

"Lieutenant Colonel John Sheppard."

"What's the date?"

"No idea. I don't know how long I was out for."

"Okay, what is the last thing you remember and what date did it occur?" Doyle rephrased.

"Everything is a little fuzzy." John confessed. "I was caught up in an explosion. I was trying to make it to a space gate. I lost control of the Jumper and got knocked out. Next thing I know I'm here."

"And the date that occurred?"

"August ish, twenty ten."

"Okay then. With time you should recover most of your memories. That's all I need from you. I'll just run the scans then take you to the briefing room."

"I know the way." John replied.

"I'm sure you do." Doyle smiled. "But my presence in the briefing has been requested."

-00-

John waited impatiently as Doyle ran his tests. With each passing minute he became more and more concerned that he saw no one he recognised in the infirmary. He was also confused by the uniforms that everyone was wearing. They were definitely not what he remembered. When Doyle finally returned John asked.

"What the hell is going on? Why don't I recognise anyone here and why are the uniforms different?"

"I promise a full explanation will be given." Doyle said. "All I'll say now is that some time has passed since you went missing."

"How much time?" John asked plucking a hair to see if it was still black.

"Colonel. You are going to have many questions, which I am not going to be able to answer. Dr McKay can. So I suggest that we go to the briefing."

"McKay?" John asked. "He's up there?"

"He is. So shall we?" Doyle asked.

"Sure." John agreed, not trusting the doctor, but impatient to see McKay.

"As I said," Doyle said as they walked down a corridor, "a few changes have happened round here."

"A few?" John questioned, noticing the different military uniforms, the changes in the corridor and the unfamiliar faces, who seemed to be staring at him. "How long exactly was I missing for?" The Colonel asked as they stepped into a transporter.

"Exactly?" Doyle asked. "I couldn't say. Although I'm sure McKay could tell you to five decimal places." The use of McKay's name once again helping to put John at ease. That was until they entered the control room and a silence swept over all the staff. Each person in the room staring at John wearing expressions of shock and awe.

"Why is every one staring at me?" John asked quietly.

"Your actions in your last battle saved hundreds if not thousands of lives. Everyone assumed you offered the ultimate sacrifice. No one here ever thought they'd see you." Doyle said climbing the steps next to John.

"So it worked? My plan?"

"To take out the armada?" Doyle questioned. "Yes it worked." He assured John as the door to the briefing room opened. As John entered he saw several strangers turn to face him before a man at the far end of the table stood and approached.

"Colonel Sheppard. It's an honour." The man said shaking John's hand. "I'm Matthew Finn, the leader of the Expedition."

"What happened to Woolsey?" John asked worried he couldn't see any of the team in the room.

"Please take a seat and we'll tell you everything." Finn said waving at an empty chair.

As John sat he asked. "Where's McKay?" Looking at Doyle he added. "You said he'd be here."

"He is." Doyle said calmly.

"No he's not." John said rescanning the room.

"Yes he is." Doyle assured him.

"No he's not." John countered.

"Yes I am." A man said.

Turning to face him John saw himself facing a stranger, who was somehow familiar.

"Colonel Sheppard." Finn said. "Meet Dr James McKay."

"Where's Rodney?"

"There's no easy way to tell you this." Finn said. "But he's dead. Everyone you knew is dead."

"What happened?"

"Time. You have been missing for over a hundred years."

* * *

 ** _-TBC_**


	2. Chapter 2

John sat in stunned silence trying to understand what was happening. He was aware of people talking, but he couldn't make out their words. Instead his mind kept concentrating on his friends, who he would never see again. Trying to force his attention back to his new present he looked round the table and saw the same look of awe as he saw in the control room. Unnerved by the expression he tried not to make eye contact with anyone. But in his efforts to avoid the awe he saw a scowl and eyes filled with something close to hatred. Focusing on the owner of the scowl he saw resentment over a strange but, again, familiar face. Turning his attention back to Finn he tried listening as the new leader tried to speak the most amount of words whilst conveying the least amount of information.

As James McKay started to speak John forced himself to listen.

"We're not entirely sure how it happened, but the craft you were in crashed on an ice moon. The moon itself was exceptionally cold and somehow that, combined with the life support, put you into a kind of cryogenic sleep. When you were found we tried to revive you as carefully as possible, but I don't mind telling you few of us thought it would work."

"Naturally we followed all the protocols…" Finn said taking over, but as he started talking John found himself looking back round the room at the strange faces.

Eventually Doyle captured Finn's attention and said.

"I think perhaps we should break for the day, it is getting late and the Colonel still needs to recover."

"Of course. I apologise." Finn smiled at John. "I will leave the Colonel in your capable care doctor." With that the leader nodded at the others round the table, most of whom reluctantly stood and filed out leaving John in the room with Doyle, McKay and the man who still scowled at John.

"So Colonel." Doyle started. "A lot to take in."

"Kinda an understatement." John commented. "One minute I am crashing and the next you are telling me I've been Buck Rodgers'ed."

"I'm sorry I don't understand." Doyle said confused.

"Don't worry about it." John said.

"I'm sure you still have many questions and I have transferred all the mission reports to your personal console, which is in your quarters."

"Thank you. Is there anyone else I am kind of connected to here?"

"Like you'd care." The scowling man said.

"Have I done something to upset you?" John asked, surprised by the level of hostility.

"This is your great grandson." McKay cut in.

"Well that's proof that this whole situation is wrong and you've confused me with someone else." John responded. "You see to have a great grandson I'd need a grandson and to have a grandson I'd need a son. I know some of my memory is a little fuzzy, but not that fuzzy. I'd remember if I had a son. Which I don't, so I can't, so he can't be my great grandson."

"John," Doyle said calmly. "Your son, John Sheppard, was born eight and a half months after you went missing."

"Again, still not possible. I wasn't even seeing anyone." John said standing and pacing. "I mean I ha-, oh."

"That's typical." The younger Sheppard said. "I guess the rumours about you were true. You know what the sad part is? She never gave up on you. She was convinced you'd return. She died a broken woman, destroyed by you. Yet you viewed your relationship as a one night stand."

"That's not fair." John protested. "I never knew." He added as he sat down feeling defeated.

"With the technology available in your time there would have been no way for you to know." Doyle said sympathetically.

"Don't make excuses for him." The younger Sheppard said.

"Look, I get that I have screwed up, a lot, but I've been out of the picture for over a hundred years. In that time how exactly have I upset you?"

"Do you have any idea what it is like to be descendant of John Sheppard? The Colonel Sheppard who sacrificed everything to save his people. The perfect John Sheppard who the masses remember for loyalty and servitude. The Colonel Sheppard whose name and cleaned record has been used for decades by politicians and Generals alike to unite a people behind the Stargate programme. Every one of your descendants have been forced to follow your footsteps and get involved in the programme, knowing we can never live up to the expectations associated with being a Sheppard." With that the younger Sheppard stormed from the room.

"What the hell was that about?" John asked

"You became a legend." The young McKay said. "It is hard to live in the shadows of a legend."

"You've managed." John pointed out.

"I had it easier, my father wasn't a physicist, which helped separate me from the legend."

"How did Rodney take that?"

"He didn't. He was already dead."

"How? When?"

"He was part of a rescue mission to find you. After weeks of searching they finally found a signal. They didn't realise it was a Wraith trap until it was too late. The whole rescue mission died."

"Then how can you exist? Rodney wasn't a father."

"His son was born almost nine months to the day after he left."

"Who else died as a result of what I did?"

"Ronon."

"How?"

"Also on the rescue mission. Most of your friends died that day. Teyla survived as she was injured and unable to go with the rescue mission. Jennifer Keller was ordered by Woolsey to stay on Atlantis as the infirmary was overrun with casualties. Both lived to their eighties. They never gave up looking for you."

"Am I a prisoner?" John asked.

"Of course not." McKay said. "You are free to go where ever you want."

"In that case, I need to go. I need some time to think." With that John left the briefing room feeling the weight and guilt of the world bearing down on him.


	3. Chapter 3

"What are you doing?" McKay asked as he and the younger Sheppard entered his lab and saw John at a console.

"Trying to figure out a way to get back."

"Get back?" James asked confused.

"To my time. To save Rodney and Ronon and everyone else who died as a result of what I did and to meet my son."

"You can't just go back. You have seen to much, you'd be interfering with the time line." McKay said.

"What are you a Federation time cop?" John asked.

"A what?"

"Never mind. Look I've done this before. Rodney helped me then."

"I know. I have seen the report." James said.

"Good, you can help me."

"Help you?"

"You are a physicist? And related to Rodney McKay?" John asked.

"Well yes."

"Then who better to help me?"

"He's not questioning his ability." The younger Sheppard pointed out. "He's questioning your ethics. If you go back and change things this reality may never exist."

"I thought you hated your life." John pointed.

"Doesn't mean I want to see my reality wiped from the universe."

"Actually our reality will probably remain unchanged. A new reality will be spawned where the Colonel goes back in time. In that reality we may not exist, but in this reality we will." McKay explained.

"Thanks for that clarification." Both Sheppard's said sarcastically, causing both men to look at each other with suspicion.

"Look." John said. "If everyone had lived long lives I probably wouldn't be doing this."

"Probably?" The younger Sheppard asked.

"I'd want to go back, but I'd like to think I'd have some self control." John shrugged. "The point is though people died because of me. People I care about. If I can do anything to stop that happening I will."

"If you go back to just after you left, in time to save the others, James McKay will never be as the events that led to his conception will never happen. Are you really willing to wipe him from history?" The younger Sheppard asked.

"I hadn't thought about that." John confessed feeling guilty. Looking at James he said. "Sorry."

"As I explained just now, I will still exist. I just won't exist in your timeline."

"And that doesn't bother you?" John asked.

"Why would it? I would never know. There is a bigger concern though."

"Which is?"

"I believe it is too big a risk to have two John Sheppards in the same time. Currently I am going through your ship's logs to see whether you travelled through time before you crashed on the moon."

"What difference does that make?" John asked.

"If you didn't and we get you back that means that you will exist both in your city and on the moon at the same time. If something happens to you on that moon that causes you not to make it here there may be a paradox. Everyone in your universe and ours could be in danger."

"Even if I did accidentally jump through time won't the problem still remain? If anyone finds me even after I am dead it will cause problems." John said.

"It will, but the probability is less. For someone to find you they would need to seek you out. Knowing the effect it could have on the timeline the only reason to do that is you have ticked them off. You are more likely to do that only in your lifetime."

"I don't know I have a knack of rubbing people up the wrong way. Take him." John said nodding towards the younger Sheppard. "I have never met him, but he looks like he wants to kill me."

"Currently there are a lot of unknowns." McKay said. "Time travel is not something we do often and there are many assumptions, some will be wrong. But we have to act in a way that will maximise everyone's chances of safety."

"So what do you suggest?" John asked.

"Until we know when you arrived on that ice moon there is no point discussing this. I will finish extracting data from the logs and get back to you." McKay said. "In the mean time, try to keep a low profile."

"And don't mention this to anyone." The younger Sheppard said.

"Why?"

"You're a hero remember? Heroes are a politician's dream. Now you are back there are many already trying to take advantage of the situation. An endorsement from you will guarantee power. Currently you are the most dangerous man alive. If one of them thinks you are trying to leave they will stop you buy any means."

"Does this mean you will help me get back?" John asked.

"It means I will do whatever is necessary to keep my city and friends safe." The younger Sheppard said. "If that is by removing you from this time so be it."


	4. Chapter 4

**A/N:** Just a reminder that John disappeared sometime after Enemy at the Gate and assumes the City got back to Pegasus.

* * *

"Good morning Colonel." McKay smiled as John entered his lab. "How are you this morning?"

"Good thanks. How's my ship?"

"Slowly revealing her secrets. The data format is not compatible with any of our systems. It has taken awhile to programme something to read the logs. But I am there now. You will be pleased to know you jumped through time before being frozen."

"So we're good?"

"Good is a bit of a stretch, but I am happier to help."

"But not happy?"

"As I said previously, this is risky. I am not going to lie and pretend to understand time travel. Even if everything went right for you physically who knows what damage we may or may not be causing to the universe. A question I often ask is why do we not see people from the future? We know it is possible. That implies that with enough time, excuse the pun," he chuckled nervously, "we should be able to crack time travel. Yet apart from you I have never met a time traveller."

"That you know of."

"True. It is possible it goes on all the time but those involved are forbidden from telling their secrets. If that is the case what you want should not cause problems. If that isn't the case though why aren't there time travellers? Is it because we risk destroying the universe." He paused and looked at John and said. "But I will help you."

"You will, why?"

"I am seeing a familiar look in your eyes. A look my Sheppard has had on occasion, a look that means you are doing this with or without my help. If you are doing it anyway the universe is already in danger. I would like to think that by helping you I may help it."

"Thank you."

"Don't thank me yet. If this goes wrong, and there is a high chance of that, you could end up at any point in time, if, in fact, you don't die in the attempt."

"That's very comforting." John said sarcastically.

"I thought you knew the dangers? If you want to pull out we can stop."

"I know the dangers." John said. "But I have been thinking as well. You sure that I am not going to destroy your time by doing this?"

"As sure as I can be." James said. "So you ready?"

"I guess."

"You remember much about your last time in the future?"

"I do."

"Good, because we will be trying something similar, only using ZPMs as the power surge."

"So I just need to travel at 88mph?"

"I'm sorry?"

"Never mind." John said. "So what do I need to do?"

"Everything is in that report. I suggest you read it."

-00-

"Colonel. How are you doing?" Finn asked as he sat at John's table a week later.

"Good, all things considered."

"So no ill effects?" Finn pressed.

"None so far." John said.

"That's good." Finn smiled. "Now, please correct me if I am off base on this, but from what I read about you I get the feeling that sitting around does not suit you."

"That's true." John conceded.

"So how do you feel about starting to work?"

"Doing what?"

"I don't know how much time you have dedicated to learning about the world you currently live in, but things here are very different from your time. We have been at war for a long time. The populous is tired."

"The legend may have grown out of hand if you think I can end a war." John pointed out.

"I am not asking you to end the war or fight. I just want you to bring hope to those who have lost it."

"How?" John asked suspiciously

"A couple of interviews a few public appearances. Your name combined with the right message could be a valuable tool."

"How am I meant to know what that message is?" John asked.

"There are plenty of people who will help you find it." Finn said. "I don't need an answer now, but please think about it."

"Sure." John said beginning to feel very uneasy about this future and his role in it.

-00-

"Colonel." Major Sheppard said. "How are you this evening?"

"I am fine, thanks." John said. "You?"

"Good. Everything is good."

"Well that's good." John said as McKay sat down and asked.

"You told him yet?"

"Yeah." Major Sheppard said.

"Really? It sounded like you were just saying good to each other." James pointed out.

"We know what it means." Major Sheppard replied.

"You do?" James asked John.

"Sure, it means we're almost good to go. The plan is drawn up and it is a case of waiting for a time to execute."

"You know the pair of you should submit yourself for study, you would help answer the nature or nurture debate." McKay pointed out.

"You can talk, I can see both of your great grandparents in you." John said.

"Really?" James asked.

"Absolutely, which is probably why you are so much more grounded that Rodney."

"So you all set?" The younger Sheppard asked, wanting to keep the conversation on track.

"I am."

"So when do you want to try?" McKay asked.

"Well, I have been thinking about that and I need to delay for a little bit." John said.

"Why?" The younger Sheppard asked.

"Because I realised you can't help me." John explained.

"Why?" McKay asked.

"If what you said is true about me being a useful weapon for politicians you will both be punished for helping me get back."

"That is our choice." McKay said.

"I want to go back to save my friends but I won't do it at your expense." John said firmly.

"I've been thinking too." The younger Sheppard said. "I heard about your meeting with Finn. It is too dangerous for you to stay."

"So he can't stay and he can't go?" McKay asked.

"Not exactly. He can't stay, but he can go, just as long as we don't help." Major Sheppard explained.

"But we have already helped." McKay said frustrated.

"Which is why you need plausible deniability and not to be around when I make the attempt." John stated.

"I don't understand." McKay said.

"It's okay. I do." The younger Sheppard confirmed. "But it will delay you."

"Understood."

"And you will need away to gain access to the control systems with us."

"Already thought of a way to do that." John smiled.

"How?" James asked.

"Which part of plausible deniability are you not getting?" Major Sheppard asked his friend.

"All you need to know is I have a way, but it could take a couple of weeks. So that just leaves getting you far away from here."

"Not a problem." The younger Sheppard said.

"But before that." John said as James McKay sat looking utterly perplexed. "I need to say something." He paused and looked at McKay. "James, what you have done in under a week, Rodney would be really proud."

"And as for you." He said looking at the Major. "I am sorry that my actions have had such an adverse influence on your life. What I did, I did to protect my people."

"I know." The Major said. "That's what makes it worse. It's easier to hate someone who did the right thing for the wrong reasons."

"I want you to know that if I make it back I intend to be a good father. I will do everything I can to protect my son."

"Make sure you do." The Major said before briefly nodding at John. He then closed his eyes for a moment before asking James.

"Ready?"

"For what?"

"That'll be a yes then." The Major said before raising his voice and saying.

"It's just as I thought. You are nothing but a self serving, arrogant, egotistical manipulator. Everyone here may think you are a hero, but I know the truth. I will not be fooled by you. Come on James, let's go." He said as he stood and left the Mess Hall, aware that all eyes were on him.


	5. Chapter 5

"Colonel Sheppard. Thank you for coming." Finn said as John entered the briefing room. John immediately noticed a suited man sitting to one side.

"The armed escort implied it wasn't optional, but you're welcome." He said carefully.

"The guards were there to ensure your safety. This is Senator Murphy." Finn said pointing to the man at his side.

"Senator." John nodded.

"It is a pleasure to meet you." Murphy smiled, the sickly smile on a politician can give. "Please take a seat."

"I understand there was a bit of a scene in the Mess Hall last night." Finn said as he carefully watched John.

"Yes, apparently not everyone feels the same way about me as you do." John said.

"I talked to Major Sheppard and Dr McKay and they believe there might be a problem."

"And you believe them?" John asked.

"As leader of the expedition I have to ensure that everything is as it should be. So I need to know, are you trying to go back to your time?" Finn asked.

"That's what he told you? So much for blood being thicker than water." John said.

"So it's true?" Finn asked looking disappointed.

"I'll admit the first few days have been hard. But I know I can't go back. It is important to maintain the timeline. I am now part of this timeline. If I were to go back I could alter the timeline or cause paradoxes. Both of which are likely to be detrimental to the timeline and the universe. Where I'm from destroying the universe is a bad thing. Unless you are McKay when apparently taking out chunks of a solar system is acceptable."

"You have done it before." Murphy pointed out. "The time travel part."

"That was different. I had no interaction with anyone in the future. This time I have."

"But you have considered it? Going back?" Finn asked.

"Of course I have considered it. Wouldn't you? Doesn't mean I would do it."

"Forgive me for being blunt but Dr McKay and Major Sheppard believe you would."

"Do they?" John asked. "I admit I discussed it with them. I didn't think that was a crime. I have lost everyone I ever knew and will never see my son. That kinda makes a man feel low. So yes I discussed it, but I would never do it. There is too much at stake." He continued his voice betraying anger.

"Colonel we did not mean to upset you, but you must realise we have a duty to protect our world." Finn said.

"Yesterday you wanted my help to do that, today you are accusing me of trying to destroy it." John said. "Basing your evidence on the word of a man who openly hates me."

"Colonel, if you want to join our fight we want you." Murphy said. "If you, the great Colonel Sheppard, says you are on our side then I believe you."

"Good." John said.

"So does that mean you will do the interviews?"

"Sure."

"Excellent, we will start the training tomorrow."

"Training?" John asked.

"We want to make sure you give the right message in the right way." Murphy explained. "It is just standard training."

"Okay. Well if that is all I may go for a run, get into shape before the interview."

"That's the spirit." Murphy smiled. "Until tomorrow Colonel."

"Until tomorrow." John said walking out of the briefing room. As he left he saw the younger Sheppard and approached.

"You are that desperate to prove to the word you are worthy of a name that you try to destroy me through exaggerations and lies? What gets me is you are prepared to take McKay down with you. I am ashamed to have you in the family." John snarled before walking off.

"He is lying." The younger Sheppard said to Finn.

"Major Sheppard, I believe for now a vacation is in your best interests. You and McKay are to report to the Invincible in one hour. You will return to Earth until such time you can be trusted to control yourselves."

"I want it stated for the record that we warned you. He can not be trusted, he will try to get back." The younger Sheppard said before storming from the control room.

-00-

That evening John watched the Invincible depart before starting to carry out his plan. Happy his great grandson and McKay were far away and blameless he looked once more at the paper McKay had given him before destroying it. He then moved to the Mess Hall and waited for Finn to approach.

"Colonel." Finn smiled. "How is the media training?"

"Enlightening." John replied. "I hadn't appreciated how much things had changed."

"I hear that you had a few problems with the script." Finn went on as Murphy joined them.

"I did." John admitted.

"It makes you uncomfortable."

"I'm a soldier not a politician. If you order me to read from that script I will."

"But?"

"But if you really think I can make a difference I think it has to seem real."

"Colonel, I appreciate what you are saying." Senator Murphy said. "However, the man the people need is the legendary Colonel Sheppard, who may not necessarily be you."

"I get that. And I have spent the last few days reading everything about him, well me, and, apart form being a little weird, I think I have learnt a lot."

"Such as?" Finn asked genuinely interested.

"According to the stories he, me, is a man of action who sees everything as black and white. Will risk everything for what he believes in."

"True, but I don't see what that has to do with the script."

"The message in the script is we need to keep fighting. We need to support you, pull together behind you for a common cause?" John asked.

"Yes."

"And you want me to sit in an office in front of a camera and deliver this message?"

"Yes."

"See that is what seems wrong. Him, me, the one thing we can all agree on is action speaks louder than words. Sitting in an office isn't right. I need to be seen contributing. Sitting behind a desk reading a script, that isn't going to cut it."

"You want to fight?" Finn asked.

"That is out of the question." Murphy chipped in. "We can not risk losing you. You are our biggest asset."

"I thought you'd say that. But I think there is a way I can help. What if I start running some training sessions?"

"That could work, the troops would love it." Finn agreed.

"I need to feel like it is contributing something worthwhile." John said.

"Okay."

"So on top of basic training I would like to run some infiltration tests."

"Some what?"

"I will try to break into areas of the city or computer systems, maybe steal a ship. I can put into action all my methods which may have been forgotten about."

"Although interesting," Murphy said, "what happens if you fail? It could be embarrassing."

"Worse case is we have evidence that the military is the best of the best and we go back to the scripted speech. Best case is we tighten up security and I get to hone my skills."

"It could work." Finn said. "Where would you want to start?"

"Already one step ahead of you. I have planned some scenarios." He said handing a datapad to Finn who scanned it then gave it to Murphy.

"You want to take control of the network?" Murphy asked.

"I'm hoping I can't. However, when was the last time it was tested?"

"I can honestly say I don't know." Finn said.

"Taking control of the network is a stretch. I was thinking of starting with stealing a Jumper and sparking a few lockdowns." John said.

"Sounds harmless enough." Murphy said. "When would you want to start?"

"Tonight. I really need to do something. I promise it won't get in the way of the media training."

"Very well Colonel. Good luck." Murphy said.

"One other thing, this is going to be more realistic without the armed escort." He John added nodding to the guards. "I get you want them to watch me, but perhaps you could request they assist me while they do it."

"I am sure we can relax the guards in the next few days." Finn said.

-00-

A week later John sat in his room ready to go home. He checked he had left nothing of importance in his quarters then radioed Finn.

"Go ahead Colonel."

"I am going to start the next test." John said.

"Another? This is the twentieth. And at this time?" Finn asked wearily.

"I have already uncovered plenty of security flaws. I will sleep better testing this one. Besides the enemy won't stop because it is late."

"Understood." Finn replied. "I will stand your escort down. Good luck. Please notify me when you have finished."

"Will do." John said killing the connection.

He then left his quarters, nodding good night to his two guards before he walked over to one of the Ancient labs and connected to the Atlantis control systems. As he did so he made a note to remind McKay to patch up the flawed security if he ever got back.

Once in the control system he triggered a citywide quarantine, one which could be locally overridden with the correct access codes. Codes he hoped only he had. And codes he prayed, now McKay was far away, no one could crack.

Happy the lockdown was initiated he attempted to use his override, sighing with relief when it worked to escape the lab. He hurried down the corridor to the armoury, once again accessing it without problems. Once there he secured a stunner, stun grenades as well as a lifesigns detector and hurried on his way.

As expected when the doors opened to the power room he was confronted by three confused scientists.

"What's going on? Is the lockdown over?" One of them asked.

"Not yet." John said before offering a weak apology and stunning them. With the threat out of the way he disconnect the spare ZPM and left the power room, heading for the control tower.

When he finally made it to the control room door he paused and mentally went through the plan once more. Happy he knew what he was doing he used the override codes again to open the door. As the door opened he threw in a couple of stun grenades and then took cover. He then patiently waited as those who had been unaffected ran to those who had been knocked out. Happy a large number of people were grouped he threw in another stun grenade and took cover once more. He then reviewed the lifesigns detector and was relieved to see just two dots moving. Taking another calming breath he raised his stunner and entered the control room, heading for the moving dots.

"Colonel Sheppard?" Finn asked as he saw him charging up the steps. "What is happening?"

"I'm going home. You should have listened to Major Sheppard and Dr McKay." With that he stunned Finn and the remaining gate technician.

"Now onto the hard part." He said to himself as he started to connected the ZPM directly to the Gate.

Once the ZPM was connected to the gate and a timer he mentally went through the plan once more, ensuring he had done everything he was meant to. Checking his watch and knowing he did not have much time before the people he stunned came to, he wrote a note which had the override code which he stuck to Finn's shirt. He then dialled the gate whilst starting the timer.

When the wormhole finally engaged he said.

"I really hope intelligence is hereditary." Then stepped into the unknown.


	6. Chapter 6

"You're alive." Rodney said as John walked through the gate.

"Perceptive as ever Rodney." John said before taking in how tired Rodney looked and adding. "How are things here?"

"Obviously not fine, but how are you here? Where have you been?" The physicist questioned, unable to believe John was in front of hm.

"Long story." John shrugged also disbelieving that he appeared to be in his own time.

"A story I suggest you start telling Colonel." Woolsey said walking down the steps.

"Before I do, what year is it?" John asked.

"Year?" McKay asked. "You've been doing it again haven't you?"

"Doing what?" Woolsey asked.

"Time travelling. So which way was it this time?" Rodney asked.

"Future."

"Of course it was, so once again you can't tell us any details." McKay said sounding disappointed.

"Sorry Rodney, but you wouldn't believe me anyway." John shrugged. "So what is the date?"

"September first, 2010." Lorne said. "You have been missing for two weeks."

"Close enough." John said relieved.

"Colonel please report to the infirmary." Woolsey said. "As soon as you are cleared please come to my office. Ronon, Lorne accompany him."

-00-

"You okay?" Ronon asked as the trio walked down to the infirmary.

"I think so. And the universe still seems to be in one piece so it looks like a win win."

"Should the universe not be in one piece?" Lorne questioned.

"Side effect of time travel is potential annihilation, apparently."

"I'll bear that in mind." Lorne said before asking. "So anything I should be worried about right now Sir?"

"Right now, no. But we do need to focus on rebuilding." John said entering the infirmary. As soon as he did a silence descended.

Jennifer looked up from her workbench wondering what had happened and saw John.

"Hey doc." He grinned.

"You found him?" She asked in disbelief.

"Not really, he found himself." Lorne said. "But Woolsey wants you to check he is who he says he is."

"Okay." Jennifer said, still trying to overcome the shock of John standing before her. "Let's get you over to the far side so people stop gawking." She said. Noticing Lorne and Ronon were also following she started to ask why only for Lorne to say.

"We have to stay with him until you have given the all clear."

"Okay." Jennifer agreed. "Let's get you verified."

"That's make me sound like a piece of software." John complained.

-00-

"Okay you two can stand down." Jennifer said smiling as she looked over at Ronon and Lorne an hour later. "He is our John Sheppard."

"Good to have you back Sir." Lorne smiled as he visibly relaxed.

"Believe me it is good to be back. You can call off the searches for me."

"Sure thing." Lorne replied.

"Perhaps you two can leave us so I can do all the other tests?" Jennifer suggested.

"Other tests?" John asked.

"The normal ones to make sure you are healthy. Shouldn't take long. Then again I don't know why I am telling you, you know that more than anyone."

"I'm not in here that much." John protested.

"Keep talking and I'll doubt the results that said you are you." Jennifer said.

"Fine, I am one of your more frequent patients. But Ronon and Rodney are worse."

"This could go on a while." Lorne commented to Ronon. "Let's leave them to it."

"Catch you in the briefing." Ronon said following the Major out.

"So how are things round here?" John asked.

"Getting better. Your plan worked, but I guess you know that."

"I also guess there was a high price." John said.

"Could have been worse." Jennifer said running scans. "Three dead. Thirty injured. Most are all on their way to recovery."

"Including Teyla?"

"Yes. She broke her arm. Clean break should heal just fine. She just needs to rest, which I am sure she'll get when she knows you are back. She took your loss badly, especially considering it was only a few months ago she lost Kanaan. She has gone to spend sometime with her people."

"How about you?"

"I'm fine."

"Really, cos you look kinda tired."

"It's been a long couple of weeks." Jennifer conceded. "But I will be fine."

"That's good but make sure you get some rest." John said before asking. "Doc while you are waiting for the results, can I talk to you. Privately."

"Of course. Anything you say in here is in confidence." Jennifer replied.

"This is kind of sensitive so could we talk in your office?" John asked.

"Umm, okay." She said confused leading him to her office where he shut the door.

"What I'm about to tell you can't leave this room."

"You have my word." Jennifer said as she waited for John to talk.

-00-

"Hey Teyla, how are you feeling?" Jennifer asked as she entered the small homestead that Teyla was living in.

"I am fine." The Athosian said. "What are you doing here?"

"I wanted to check on you and Torren and run a few tests."

"I don't need any more tests."

"Humour me, then I will leave you in peace."

"Fine." Teyla said.

"How's Torren?" Jennifer asked looking over at the sleeping child as she drew a blood sample from Teyla.

"He is okay. He is fortunate to be too young to understand."

"And you?"

"I am fine."

"And the truth?" Jennifer asked causing Teyla to look at her and say, her voice almost resigned.

"I think I'm pregnant."

"I know." Jennifer said.

"How?"

"Long story. Let me take a couple more samples then I will fill you in."

Once she was done she said. "I am going to take these back to Atlantis for testing. Why don't I take Torren with me?"

"Why would I want you to do that?" Teyla asked perplexed.

"Because outside there is someone you really need to speak to. Trust me on this." Jennifer said picking up the infant.

"Who?" Teyla asked.

"Sheppard. He's back and outside. I've got Torren, go."

"John is alive?" Teyla questioned in disbelief.

"He is. He's been jumping in time again. But he is back and fine and wants to see you. So I am going to take Torren back to the city. You two need to talk."

As Teyla left her temporary home she saw John leaning against a tree.

"John?" She asked in disbelief.

On hearing Teyla's voice John immediately straightened and strode towards the Athosian. Once he had reached her he cupped her face in his hands and kissed her.

When he broke the kiss Teyla looked at him, her eyes full of sorrow, confusion and disbelief.

"John? Is that really you?"

"I'm here and I'm not going anywhere." He said kissing her once more.

 _ **-The End**_

* * *

 _ **A/N:**_ Thanks for reading and reviewing.


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